Contacts of the helix formed by residues 835 - 850 (chain E) in PDB entry 3T06
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 835 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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777E ARG* 3.8 55.9 + - + +
780E PRO* 6.1 2.0 - - + -
831E GLN 4.8 4.7 + - - +
832E PHE 4.9 0.4 + - - -
834E SER* 1.3 84.4 + - - +
836E GLN* 1.3 59.7 + - - +
837E SER* 3.4 2.0 - - - -
838E ILE* 2.9 57.8 + - + +
839E ALA* 3.1 12.5 + - - -
842E LEU* 4.3 13.9 - - + +
927E THR* 4.0 15.0 - - + -
931E HIS* 5.1 10.5 + + + -
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Residues in contact with GLN 836 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777E ARG 5.6 1.3 - - - -
778E LEU* 5.2 5.0 + - + +
832E PHE* 3.5 33.6 + - - +
833E CYS* 3.2 23.4 + - - +
835E TYR* 1.3 77.0 - - - +
837E SER* 1.3 63.8 + - - +
839E ALA* 3.2 9.2 + - + +
840E LEU* 3.0 38.6 + - + +
875E ILE* 3.2 50.2 + - + +
876E ILE* 3.9 17.7 - - - +
879E MET* 5.8 0.9 - - - +
72F LEU* 5.7 6.8 - - + +
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Residues in contact with SER 837 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833E CYS 4.7 0.8 + - - -
834E SER 5.2 0.8 + - - -
835E TYR 3.2 0.8 + - - -
836E GLN* 1.3 77.2 - - - +
838E ILE* 1.3 78.3 + - - +
840E LEU* 3.6 8.5 + - - +
841E GLU* 3.4 21.0 + - - +
928E GLU* 3.1 27.7 + - - +
72F LEU* 3.7 21.0 - - - +
75F PRO* 6.3 2.9 - - - -
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Residues in contact with ILE 838 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834E SER 5.3 0.4 - - - +
835E TYR* 2.9 50.5 + - + +
837E SER* 1.3 84.4 - - - +
839E ALA* 1.3 67.5 + - - +
841E GLU* 3.3 6.3 + - + +
842E LEU* 3.2 35.9 + - + +
927E THR* 5.1 4.0 - - + -
928E GLU* 4.8 13.9 - - + +
931E HIS* 3.8 47.6 - - + +
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Residues in contact with ALA 839 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777E ARG* 4.1 18.6 - - + +
778E LEU* 4.0 28.7 - - + +
835E TYR* 3.1 17.7 + - + +
836E GLN* 3.6 10.5 - - - +
838E ILE* 1.3 79.5 - - - +
840E LEU* 1.3 57.8 + - - +
842E LEU* 3.2 11.3 + - - +
843E ILE* 2.9 29.5 + - - +
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Residues in contact with LEU 840 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778E LEU* 4.7 8.1 - - + -
836E GLN* 3.0 30.9 + - + +
837E SER* 4.0 7.6 - - - +
839E ALA* 1.3 77.1 - - - +
841E GLU* 1.3 58.4 + - - +
843E ILE* 3.2 9.6 + - + +
844E LYS* 3.1 20.3 + - - +
871E LEU* 3.9 27.6 - - + -
872E ARG* 3.3 53.7 + - + +
875E ILE* 3.9 26.2 - - + -
876E ILE* 6.2 1.1 - - + -
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Residues in contact with GLU 841 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837E SER 3.4 10.5 + - - +
838E ILE* 3.3 9.0 + - - +
839E ALA 3.3 0.8 - - - -
840E LEU* 1.3 73.6 - - - +
842E LEU* 1.3 69.9 + - + +
843E ILE 3.1 1.6 - - - -
844E LYS* 3.3 38.3 + - - +
845E THR* 3.3 26.6 + - - +
872E ARG* 4.6 7.0 + - - +
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Residues in contact with LEU 842 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774E GLU* 6.0 1.8 - - - +
777E ARG* 5.4 8.5 - - - +
835E TYR* 4.3 20.0 - - + +
838E ILE* 3.2 22.6 + - + +
839E ALA* 3.2 10.7 + - - +
841E GLU* 1.3 82.3 - - + +
843E ILE* 1.3 64.9 + - + +
845E THR* 4.0 10.1 - - - +
846E LYS* 3.4 25.2 + - - +
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Residues in contact with ILE 843 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764E MET* 5.4 1.1 - - + -
770E MET* 3.7 26.9 - - + -
778E LEU* 4.2 23.6 - - + -
839E ALA 2.9 14.6 + - - +
840E LEU* 3.2 17.9 + - + +
841E GLU 3.1 0.4 - - - -
842E LEU* 1.3 82.6 - - + +
844E LYS* 1.3 69.8 + - - +
846E LYS* 3.6 7.4 + - + +
847E GLN* 3.3 34.6 + - - +
853E PHE* 3.8 21.5 - - + -
857E MET* 5.7 2.9 - - - -
871E LEU* 4.7 16.6 - - + -
872E ARG* 4.9 4.5 - - - +
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Residues in contact with LYS 844 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840E LEU 3.1 7.0 + - - +
841E GLU* 3.5 37.3 + - - +
843E ILE* 1.3 77.6 - - - +
845E THR* 1.3 62.7 + - - +
847E GLN* 2.9 24.5 + - - +
848E ARG* 3.0 14.7 + - - +
872E ARG* 3.6 32.8 - - - +
76F ASP* 4.6 12.8 + - - +
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Residues in contact with THR 845 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841E GLU* 3.3 18.3 + - - +
842E LEU* 4.1 10.2 - - - +
843E ILE 3.3 0.2 - - - -
844E LYS* 1.3 78.4 - - - +
846E LYS* 1.3 64.0 + - - +
848E ARG* 3.0 33.4 + - - +
849E LYS* 3.0 46.1 + - + +
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Residues in contact with LYS 846 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769E LEU 4.8 0.2 - - - +
770E MET* 4.1 32.2 - - + +
771E PRO* 4.2 3.2 - - - +
774E GLU* 2.9 39.0 + - - -
842E LEU* 3.4 18.1 + - - +
843E ILE* 3.9 7.2 - - + +
844E LYS 3.3 0.6 - - - -
845E THR* 1.3 79.4 - - - +
847E GLN* 1.3 57.1 + - - +
849E LYS* 4.6 3.1 - - - +
850E GLU* 2.8 69.8 + - - +
853E PHE* 3.6 28.6 - - + -
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Residues in contact with GLN 847 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843E ILE* 3.3 26.8 + - - +
844E LYS* 2.9 14.0 + - - +
846E LYS* 1.3 76.9 - - - +
848E ARG* 1.3 60.7 + - - +
849E LYS 3.1 3.2 + - - -
850E GLU 3.6 3.5 - - - +
853E PHE* 3.7 17.7 - - + -
854E GLN* 3.2 45.7 + - + +
857E MET* 3.8 29.0 - - + +
858E GLN* 6.1 1.0 - - - +
861E GLU* 5.1 6.0 + - - +
870E GLN* 5.9 3.1 + - - +
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Residues in contact with ARG 848 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844E LYS 3.0 11.2 + - - +
845E THR* 3.0 25.4 + - - +
847E GLN* 1.3 76.4 - - - +
849E LYS* 1.3 88.6 + - - +
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Residues in contact with LYS 849 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773A GLU* 3.8 19.6 - - - +
845E THR* 3.0 35.9 + - + +
846E LYS* 4.3 1.8 - - - +
847E GLN 3.1 0.6 - - - -
848E ARG* 1.3 103.2 - - - +
850E GLU* 1.3 67.9 + - + +
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Residues in contact with GLU 850 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A PRO* 3.3 39.2 - - + +
773A GLU* 3.8 7.6 - - + +
774A GLU* 4.9 1.6 - - - +
769E LEU 4.3 8.8 - - - +
846E LYS* 2.8 60.1 + - + +
847E GLN 3.6 8.3 - - - +
849E LYS* 1.3 79.3 - - + +
851E SER* 1.3 63.4 + - - +
852E ARG* 4.6 3.1 - - + +
853E PHE* 3.8 16.7 + - + +
854E GLN* 3.4 15.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il